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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
..., and translation efficiency. In contrast, ALE-APA results from multiple PASs located in alternative terminal exons, which could lead to the production of truncated protein isoforms (Mariella et al. 2019; Goering et al. 2021). These alternatively polyadenylated mRNAs greatly expand the diversity of transcripts...
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Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
- Marcin P. Sajek,
- Danielle Y. Bilodeau,
- Michael A. Beer,
- Emma Horton,
- Yukiko Miyamoto,
- Katrina B. Velle,
- Lars Eckmann,
- Lillian Fritz-Laylin,
- Olivia S. Rissland,
- and Neelanjan Mukherjee
Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
...studies as well as new therapeutic angles to target eukaryotic pathogens.Cleavage and polyadenylation (CPA) are key steps in eukaryotic mRNA maturation, specifying the 3′ end of the transcript and the addition of the poly(A) tail. Required for the proper expression of nearly all mRNAs, the site of pre-mRNA...
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Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
....ji@northwestern.eduAbstract3′-end cleavage and polyadenylation is an essential process for eukaryotic mRNA maturation. In yeast species, the polyadenylation signals that recruit the processing machinery are degenerate and remain poorly characterized compared with the well-defined regulatory elements in mammals. Here we...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...in other aspects of plant development, such as imprinting by regulating MEDEA, a histone methyltransferase of the polycomb repressive complex 2 (PRC2) (Satyaki and Gehring 2017), in recombination patterns during meiosis, where mCHG limits heterochromatin rearrangements (Underwood et al. 2018...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...of chromatin biology: transcription, gene regulation, DNA repair, DNA replication, mitosis and meiosis, and many others) (Jenuwein and Allis 2001), which are almost universally invariant across all eukaryotes.Eukaryotic histones trace their ancestry to Archaea (Woese and Fox 1977), which is the half...
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Method: CodonBERT large language model for mRNA vaccines
- Sizhen Li,
- Saeed Moayedpour,
- Ruijiang Li,
- Michael Bailey,
- Saleh Riahi,
- Lorenzo Kogler-Anele,
- Milad Miladi,
- Jacob Miner,
- Fabien Pertuy,
- Dinghai Zheng,
- Jun Wang,
- Akshay Balsubramani,
- Khang Tran,
- Minnie Zacharia,
- Monica Wu,
- Xiaobo Gu,
- Ryan Clinton,
- Carla Asquith,
- Joseph Skaleski,
- Lianne Boeglin,
- Sudha Chivukula,
- Anusha Dias,
- Tod Strugnell,
- Fernando Ulloa Montoya,
- Vikram Agarwal,
- Ziv Bar-Joseph,
- and Sven Jager
Genome Res. July 2024 34: 1027-1035; Published in Advance July 1, 2024, doi:10.1101/gr.278870.123
...data sets. Table 1 presents the data sets and the mRNA properties. As can be seen, these included a diverse set of downstream tasks related to mRNA translation, stability, and regulation. In addition, these data sets represent a range of molecules, including newly published data sets for recombinant...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...splicing, and 3′ end cleavage and polyadenylation—can be alternatively regulated to create a multitude of mRNA isoforms from a single gene region (Fig. 1A). Importantly, splicing occurs at specific splice sites on an mRNA (delineated by strong sequence motifs), but there is more stochasticity in the choice...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...and developmental stages, and identify differentially regulated mRNA decay throughout embryonic development. We identify transcript features that are correlated with mRNA stability and find that mRNA decay rates are associated with distinct peaks in gene expression over time. Moreover, we provide evidence that...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...role in human health by degrading mRNAs containing PTCs, which drive diverse diseases (Mort et al. 2008). NMD also regulates the abundance of ∼5%–20% of endogenous transcripts in animals, making NMD broadly relevant for gene expression (Mendell et al. 2004; Rehwinkel et al. 2005; Wittmann et al. 2006...
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Research: Vascular histone deacetylation by pharmacological HDAC inhibition
- Haloom Rafehi,
- Aneta Balcerczyk,
- Sebastian Lunke,
- Antony Kaspi,
- Mark Ziemann,
- Harikrishnan KN,
- Jun Okabe,
- Ishant Khurana,
- Jenny Ooi,
- Abdul Waheed Khan,
- Xiao-Jun Du,
- Lisa Chang,
- Izhak Haviv,
- Samuel T. Keating,
- Tom C. Karagiannis,
- and Assam El-Osta
Genome Res. August 2014 24: 1271-1284; Published in Advance April 14, 2014, doi:10.1101/gr.168781.113
...(data not shown). There were no statistically significant changes in DNA methylation or H3K9me3. Further analysis revealed histone deacetylation changes associated with mRNA and noncoding RNA (ncRNA). We found significant changes at genes that code for ncRNAs (Fig. 1E).While both increased and reduced...

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